// ==================================================================================
// Shared Genomics Project MPI Codebase
// Version 1.0 30/04/2010
//
// (c) 2010 University of Manchester all rights reserved
//
// This file is distributed under the GNU General Public License, Version 2.  
// Please see the file COPYING.txt for more details
// ==================================================================================

#ifndef _SUFFIXES_H_
#define _SUFFIXES_H_

#ifdef __cplusplus
extern "C" {
#endif

/*!
\file
\ingroup	gio
\brief		Data/Result File Suffixes
*/

/*! 
\brief PLINK-compatible Pedigree File 
\details Contains Allelic information of people in a genomic data-set.
\sa pedfile.h
*/
#define SUFFIX_PED_FILE ".ped"

/*! 
\brief PLINK-compatible Genomic Map File 
\details Contains list of SNPs in a genomic data-set.
\sa mapfile.h
*/
#define SUFFIX_MAP_FILE ".map"

/*! 
\brief PLINK-compatible Phenotype File 
\details Contains list of pheonotype/response variables data for people in a genomic data-set.
\sa phefile.h
*/
#define SUFFIX_PHE_FILE ".phe"

/*! 
\brief Output Suffix for the PMODEL program
\sa pmodel_main()
*/
#define SUFFIX_MODEL_FILE ".model.csv"

/*!
\brief Output Suffix for the Single Assoc Scan programs
\sa passoc_bt_main()
\sa passoc_qt_main()
*/
#define SUFFIX_ASSOC_FILE ".assoc.csv"

/*!
\brief Permutation Indices File
\sa permfile.h
*/
#define SUFFIX_PERM_FILE ".perm.dat"

/*!
\brief Binary Encoded samples array 
\sa sample.h
*/
#define SUFFIX_SAMPLE_FILE ".samples.dat"

/*!
\brief Bit-string encoded, SNP-major Allelic data file
\sa spedfile.h
*/
#define SUFFIX_SPED_FILE ".sped.dat"	

/*!
\brief Byte encoded, SNP-major Allelic data file
\sa bpedfile.h
*/
#define SUFFIX_BPED_FILE ".bped.dat"

/*!
\brief A Fragment of Byte encoded, SNP-major Allelic data file
\sa SUFFIX_BPED_FILE
\sa bpedfile_write_filtered()
*/
#define SUFFIX_FBPED_FILE ".fbped.dat"

/*! 
\brief Binary-encoded Genomic Map File 
\details Contains list of SNPs in a genomic data-set.
\sa bmapfile.h
*/
#define SUFFIX_BMAP_FILE ".bmap.dat"

/*!
\brief Bit-string encoded, Individual-major Allelic data file
\sa ipedfile.h
*/
#define SUFFIX_IPED_FILE ".iped.dat"

/*! \brief Temporary Output Suffix for epistasis programs */
#define SUFFIX_LOCAL_EPI_FILE "_epi.dat"

/*! \brief Local 'best' pair-wise epistasis output file */
#define SUFFIX_LOCAL_BEPI_FILE "_bepi.dat" 

/*! \brief Reasons for SNP removal from a filtered genomic data-set. */
#define SUFFIX_FILTER_LOG ".flog.txt"

/*! \brief Filter Settings */
#define SUFFIX_FILTER_SETTINGS ".fslog.txt" 

/*! \brief Merge Log, i.e. which MPI ranks failed to produce any data */
#define SUFFIX_MERGE_LOG ".mlog.txt" // Merge Log (Mlog file)

/*! \brief Epistasis - supposed significant hits (text file) */
#define SUFFIX_EPI_FILE ".epi.csv"   

/*! \brief Epistasis - supposed significant hits (binary file) */
#define SUFFIX_EPI_FILE2 ".epi.dat" 

/*! \brief Epistasis - permutation counts for supposed significant hits */
#define SUFFIX_REPI_FILE ".repi.dat"   // The randomised counts for significant hits.

/*! \brief Epistasis - final output file for supposed significant hits */
#define SUFFIX_FEPI_FILE ".fepi.csv"

/*! \brief Epistasis - The best pair-wise interactions found at each SNP in a data-set. */
#define SUFFIX_BEPI_FILE ".bepi.csv"

/*! \brief Epistasis - Randomised best pair-wise interactions count data */
#define SUFFIX_RBEPI_FILE ".rbepi.dat"   

/*! \brief Epistasis - The final output file of best pair-wise interactions found at each SNP in a data-set. */
#define SUFFIX_FBEPI_FILE ".fbepi.csv"

/*! 
\brief Random Seed File 
\sa seedfile.h
*/
#define SUFFIX_RSEED_FILE ".rseed.dat"

/*! 
\brief 'Sorted' CSV File
\sa seedfile.h
*/
#define SUFFIX_SORTED_FILE ".sort.csv" 

/*! 
\brief Person Missingness File
\sa missingness.h
*/
#define SUFFIX_PERSON_MISSINGNESS ".pm.dat" 

/*!
\brief Founders File
\sa foundersfile.h
*/
#define SUFFIX_FOUNDERS_FILE ".ff.dat"

/*!
\brief SNPs to Delete
\sa bfilter.h
*/
#define SUFFIX_SNP_TO_DEL ".std.dat"

/*!
\brief Persons to Delete
\sa bfilter.h
*/
#define SUFFIX_PERSON_TO_DEL ".ptd.dat" 

/*!
\brief Filtered Data-set Dimensions
\sa pformat_write_filter_dims()
*/
#define SUFFIX_DATASET_DIMS ".dims.txt"

/*!
\brief Double Array File
\sa doublefile.h
*/
#define SUFFIX_DOUBLE_FILE ".d.dat"

/*!
\brief Strata or Layer (SOL) File
\sa solfile.h
*/
#define SUFFIX_SOL_FILE ".sol.dat"

/*!
\brief PCMH Output File
\sa pcmh_bt_main()
*/
#define SUFFIX_CMH_FILE ".cmh.csv"

/*!
\brief Adjusted P-value Array
\sa adjusted.h
*/
#define SUFFIX_PADJ_FILE ".adj.dat"

/*! 
\brief Summary Statistics for a 'raw' Genomic Data-set
\sa bpedfile_write_summary_and_copy()
*/
#define SUFFIX_BPED_SUMMARY ".summary.txt"

/*! \brief Epistasis - Raw Epistasis Data (Version 2.0) */
#define SUFFIX_RAW_EPI_FILE ".epi.raw.dat"

/*! \brief Record the seed value used to initialise the PRNG code.  */
#define SUFFIX_RSEED_LOG_FILE ".rseed.txt"

/*! \brief A PLINK-compatible transposed pedigree file */
#define SUFFIX_TPED_FILE ".tped"

/*! \brief A PLINK-compatible Family/Phenotype (TFAM) file */
#define SUFFIX_TFAM_FILE ".tfam"

/*! \brief A R-genetics Phenotype/gender file */
#define SUFFIX_GPHE_FILE ".gphe.dat"

/*! \brief A simple map file for SNP data import into R */
#define SUFFIX_SMAP_FILE ".smap.txt"

/*! \brief A Binary Count (ABC) file of permutation results.  */
#define SUFFIX_ABC_FILE ".abc.dat"

/*!
\brief SNPs to MAF flip
\sa bfilter.h
*/
#define SUFFIX_SNP_TO_FLIP ".stf.dat"

#ifdef __cplusplus
}
#endif

#endif // _SUFFIXES_H_
